At least one (not all) Spearman correlations across replicates is low using a barcode threshold per oligo of 10! Spearman correlation of DNA is 0.95, RNA is 0.60 and DNA/RNA ratio is 0.65. Minimum allowed values are 0.85, 0.95, and 0.75.
MPRAsnakeflow experiment QC report
WarningLow correlation warning!
Overall quality metrics
Table explanation
- median rna read count: Median of RNA read count for oligos that passed filtering to determine sufficient coverage in terms of read count. Value is the median of all replicates.
- median barcodes passing filtering: Median number of barcodes across tested sequences that passed filtering to determine if there was sufficient barcode to oligo coverage. Value is the median of all replicates.
- pearson correlation: The correlation of log2 RNA/DNA ratios across tested sequences as a measure of replicable activity signal. Value is the median of replicate comparisons using only oligos with >= 10 barcodes.
- fraction oligos passing: Fraction of tested sequences that passed filtering of the mappable sequences to determine if the designed library was sufficiently recovered. Value is the median of all replicates and using only oligos with >= 10 barcodes.
| median barcodes passing filtering | median rna read count | pearson correlation | fraction oligos passing |
|---|---|---|---|
| 67 | 641 | 0.85 | 0.92 |
DNA over RNA counts
Plotting normalized counts of DNA vs RNA (median across replicates). Only oligos within all replicates are shown. We should see a variation within the RNA count data (along the y axis). If count data between RNA and DNA is highly correlated (e.g. follows the identity line) there is no variation between designed oligos. This is an indication that RNA is inflated with DNA and the DNA digestion before creating cDNA did not work as expected.
Oligo correlation
Oligo correlation plots of DNA, RNA and DNA/RNA ratios across replicates. First tab shows plots using (in average) 54114 oligos with a minimum number of 10 barcodes. Second tab shows all 58440 oligos that have assigned barcodes.
| Condition | A | B | #Oligos A | #Oligos B | #Oligos Joined | DNA spearman | RNA spearman | Ratio spearman | DNA log2 pearson | RNA log2 pearson | Ratio log2 pearson |
|---|---|---|---|---|---|---|---|---|---|---|---|
| A549 | 1 | 2 | 54791 | 54705 | 54328 | 0.96 | 0.63 | 0.67 | 0.96 | 0.82 | 0.84 |
| A549 | 1 | 3 | 54791 | 54775 | 54367 | 0.96 | 0.64 | 0.67 | 0.96 | 0.83 | 0.85 |
| A549 | 1 | 4 | 54791 | 54339 | 54066 | 0.96 | 0.62 | 0.67 | 0.96 | 0.82 | 0.84 |
| A549 | 1 | 5 | 54791 | 54333 | 54057 | 0.96 | 0.60 | 0.65 | 0.95 | 0.81 | 0.84 |
| A549 | 2 | 3 | 54705 | 54775 | 54305 | 0.96 | 0.66 | 0.71 | 0.96 | 0.86 | 0.88 |
| A549 | 2 | 4 | 54705 | 54339 | 54045 | 0.96 | 0.64 | 0.70 | 0.96 | 0.84 | 0.86 |
| A549 | 2 | 5 | 54705 | 54333 | 54026 | 0.96 | 0.63 | 0.70 | 0.95 | 0.84 | 0.87 |
| A549 | 3 | 4 | 54775 | 54339 | 54054 | 0.96 | 0.65 | 0.71 | 0.96 | 0.85 | 0.87 |
| A549 | 3 | 5 | 54775 | 54333 | 54061 | 0.96 | 0.64 | 0.70 | 0.96 | 0.86 | 0.87 |
| A549 | 4 | 5 | 54339 | 54333 | 53831 | 0.95 | 0.61 | 0.70 | 0.95 | 0.84 | 0.86 |
| Condition | A | B | #Oligos A | #Oligos B | #Oligos Joined | DNA spearman | RNA spearman | Ratio spearman | DNA log2 pearson | RNA log2 pearson | Ratio log2 pearson |
|---|---|---|---|---|---|---|---|---|---|---|---|
| A549 | 1 | 2 | 58718 | 58727 | 58502 | 0.95 | 0.60 | 0.63 | 0.91 | 0.73 | 0.73 |
| A549 | 1 | 3 | 58718 | 58716 | 58480 | 0.95 | 0.61 | 0.64 | 0.91 | 0.74 | 0.74 |
| A549 | 1 | 4 | 58718 | 58649 | 58423 | 0.95 | 0.58 | 0.64 | 0.90 | 0.71 | 0.73 |
| A549 | 1 | 5 | 58718 | 58638 | 58413 | 0.95 | 0.57 | 0.62 | 0.90 | 0.72 | 0.73 |
| A549 | 2 | 3 | 58727 | 58716 | 58497 | 0.95 | 0.63 | 0.67 | 0.91 | 0.77 | 0.77 |
| A549 | 2 | 4 | 58727 | 58649 | 58436 | 0.95 | 0.61 | 0.66 | 0.90 | 0.74 | 0.75 |
| A549 | 2 | 5 | 58727 | 58638 | 58433 | 0.95 | 0.60 | 0.66 | 0.90 | 0.75 | 0.76 |
| A549 | 3 | 4 | 58716 | 58649 | 58426 | 0.95 | 0.61 | 0.67 | 0.90 | 0.75 | 0.76 |
| A549 | 3 | 5 | 58716 | 58638 | 58421 | 0.95 | 0.61 | 0.66 | 0.90 | 0.77 | 0.77 |
| A549 | 4 | 5 | 58649 | 58638 | 58378 | 0.94 | 0.58 | 0.66 | 0.90 | 0.74 | 0.76 |